Refactoring small mol; Fix missing 'entity B's

geneontology · Jun 17, 2021 · 755091d · 755091d
1 parent 53e2189
commit 755091d
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Showing 3 changed files with 44 additions and 26 deletions.
diff --git a/entity_models.py b/entity_models.py
@@ -23,6 +23,9 @@ def class_id(self):
     def is_complex(self):
         return isinstance(self, SignorComplex)
 
+    def is_small_mol(self):
+        return isinstance(self, SignorSmallMolecule)
+
     def __eq__(self, other):
         if isinstance(other, SignorEntity):
             return self.id == other.id and self.name == other.name

diff --git a/pathway_connections.py b/pathway_connections.py
@@ -191,6 +191,19 @@ def __str__(self):
     def print(self):
         print(self)
 
+    def declare_a_to_mechanism(self, model, eco_code):
+        # Declare entity A and mechanism
+        self.declare_a(model)
+        if self.a_is_small_mol():
+            # Skip enabled_by stmt for small molecules
+            self.mechanism["uri"] = self.entity_a.uri  # Entity A is_activator
+            return
+        self.mechanism["uri"] = model.declare_individual(self.mechanism["term"])
+        # Emit mechanism -enabled_by -> entity_a
+        self.enabled_by_stmt_a = model.writer.emit(self.mechanism["uri"], ENABLED_BY, self.entity_a.uri)
+        evidence = self.gocam_evidence(eco_code)
+        return model.add_axiom(self.enabled_by_stmt_a, evidence=evidence)
+
     def declare_entities(self, model):
         self.declare_a(model)
         self.declare_b(model)
@@ -237,6 +250,16 @@ def a_is_complex(self):
     def b_is_complex(self):
         return self._is_complex(self.entity_b)
 
+    @staticmethod
+    def _is_small_mol(entity: SignorEntity):
+        return entity.is_small_mol()
+
+    def a_is_small_mol(self):
+        return self._is_small_mol(self.entity_a)
+
+    def b_is_small_mol(self):
+        return self._is_small_mol(self.entity_b)
+
     def clone(self):
         new_connection = PathwayConnection(self.entity_a, self.entity_b, self.mechanism["name"], self.effect,
                                            self.direct, self.relation, self.references, self.linenum)

diff --git a/pathway_importer.py b/pathway_importer.py
@@ -86,22 +86,8 @@ def generate_model(filename, title):
 
     # fill in regulated activities
     for pc in p_connections.connections:
-
-        # Declare entity A and mechanism
-        pc.declare_a(model)
-        pc.mechanism["uri"] = model.declare_individual(pc.mechanism["term"])
-        # Emit mechanism -enabled_by -> entity_a
-        pc.enabled_by_stmt_a = model.writer.emit(pc.mechanism["uri"], ENABLED_BY, pc.entity_a.uri)
-        date = pc.date
-        if date is None:
-            date = str(datetime.date.today())
-        contributors = []
-        if pc.annotator:
-            contributors = [pc.annotator]
-        evidence = GoCamEvidence(EXP_ECO_CODE, ["PMID:" + pmid for pmid in pc.references],
-                                 date=date, contributors=contributors)
-        axiom_a = model.add_axiom(pc.enabled_by_stmt_a, evidence=evidence)
-        # model.add_evidence(axiom_a, "EXP", ["PMID:" + pmid for pmid in pc.references])
+        # Setup
+        pc.declare_a_to_mechanism(model, EXP_ECO_CODE)
 
     # Now that the a's are declared, go check on the b's.
     for pc in p_connections.connections:
@@ -114,24 +100,30 @@ def generate_model(filename, title):
         regulatory_relation = pc.relation
         evidence = pc.gocam_evidence(EXP_ECO_CODE)
         if len(entity_b_pcs) == 0:
+            # BPC was likely filtered out due to BPC.entity B not being acceptable type (e.g. phenotype)
+            # Declare pc.entity B? A and B should be valid by this point
+            # A protein -> B complex
+            # A complex -> B phenotype
+            # Create and load new PC
             print("No downstream pathway_connections for", pc)
         for bpc in entity_b_pcs:
             participant_relation = HAS_INPUT
             is_small_mol_catalysis = False
             # catalytic activity
-            if pc.mechanism["term"] == "GO:0003824" and isinstance(pc.entity_b, SignorSmallMolecule):
+            if pc.mechanism["term"] == "GO:0003824" and pc.b_is_small_mol():
                 is_small_mol_catalysis = True
                 if pc.effect.startswith("up-regulates"):
                     participant_relation = HAS_OUTPUT
-            # mechanism -has_input/output-> entity_b
-            has_input_triple = (mechanism_uri, participant_relation, bpc.entity_a.uri)
-            if len(model.triples_by_ids(*has_input_triple)) == 0:
-                model.writer.emit(*has_input_triple)
-            has_input_axiom = model.find_or_create_axiom(*has_input_triple)
-            model.add_evidence(has_input_axiom, evidence=evidence)
-            if is_small_mol_catalysis:
-                # Skip adding causal relation
-                continue
+            if not pc.a_is_small_mol():
+                # mechanism -has_input/output-> entity_b
+                has_input_triple = (mechanism_uri, participant_relation, bpc.entity_a.uri)
+                if len(model.triples_by_ids(*has_input_triple)) == 0:
+                    model.writer.emit(*has_input_triple)
+                has_input_axiom = model.find_or_create_axiom(*has_input_triple)
+                model.add_evidence(has_input_axiom, evidence=evidence)
+                if is_small_mol_catalysis:
+                    # Skip adding causal relation
+                    continue
 
             # Add intermediary biological process for these regulatory mechanisms
             intermediary_bp = None